Goron Mines

Skip the First Two Flame Jets

Instead of turning off the first two flame jets, simply walk into them and take damage, then quickly roll through them while temporarily invincible. You'll also be fine if you hit the fire at the end of your roll. If you're in the middle of a roll however you will get smashed into the lava.

Skip the Third Flame Jet

After passing the second flame jet, you can Long Jump Attack across the lava. Simply take out the Gale Boomerang, target over the giant switch that unlocks the next room and jump across when the boomerang is over the switch.

Second Room Strategy

Quickly roll to the right to land on the platform below and grab the key, then quickly make your way to the rotating platforms. If done fast enough, should be able to make your way across the platforms without having to wait for them.

Key Shard & Magnetic Ceiling Skip

It is possible to get up to the middle part of the main magnet mechanism room without going through the three rooms that normally connect the lower and middle portions. This skips the first small key, the first goron elder, and the entire magnetic ceiling room. AKA Kitty Jump/Kitty Climb :]

With Out of Bounds Climb

1. Jump onto the railing
2. Walk carefully to the right side of the railing at the corner; look for the right side of Link's left foot to be roughly aligned with the right side of the railing texture
3. Enter first person and aim the camera such that the left side of the screen covers the left rivets on the wall between the two metal beams (see video)
4. Sidehop right to get past the invisible wall; if done correctly, Link will jitter momentarily midair
5. Walk forward until Link is stopped, then slash (while still holding forward) to get past the block
6. Continue walking forward into the corner. Go into first person and aim slightly more than halfway into the corner. Then perform a jumpslash. If link doesn't go through the corner, you were aiming too far left. If Link goes through the corner but then slips off, you were aiming too far right.
7. Slowly walk into the final corner (keep left to avoid slipping off)
8. Go into first person and aim such that the upper left corner of the screen slightly covers the left metal beam (see video)
9. Target and slash (without holding a direction) to pop into the railing
10. Turn 45 degrees left and then pull out the boomerang (if you pull out the boomerang and Link falls out you didn't turn elft enough)
11. Aim as shown in the video below.
12. Target and perform two back hops to pop up to the 2nd level. This is by far the finnickiest part of the whole trick and is not 100% consistent.

With Magic Armor Moonboots Backslice

Discovered by pokemongenius, setup by jeez

From on top of the doorframe in the second room, using a moonboots backslice with a boomerang bomb boost it's possible to get onto the fence of the next level up, skipping the small key, the first goron elder, and the entire magnetic ceiling. This saves ~2.5 minutes.

See SD ZSR for a detailed explanation

LJA From Magnetic Ceiling Room Exit

Discovered by Bewildebeest, setup by gymnast86

1. Open the door as far to the right as possible
2. Target walk into the bottom left corner of the door frame
3. Perform 3 Dry Rolls (wait for Link to stop between each one)
4. Using the hawkeye, aim like in the image below. Put the up arrow of the hawkeye view one visual tic up and in from the bottom left corner of the roughly box shaped cue.
5. Hold the boomerang button and create 5 targets with the boomerang
6. Perform the LJA

Stone Slab Timesaver

In the third room of the dungeon, instead of pulling the stone slab out all the way, pull it back three times, then quickly walk around to the right side of the slab and roll into it to clip inside of the slab. Keep rolling forward until your pushed out on the other side of the wall, and make your way to the door.

Underwater Key Room Strategies

Grab the underwater key in this room, then swim over to the underwater block. Instead of pushing the block, simply dive under the fench with the iron boots and swim up to clip past it.
You can skip activating the second Magnetic pull by using an LJA over to the crystal switch aiming at the pipe.

Skip Cutting Down The Bridge

You can skip cutting the ropes and dropping the bridge with Long Jump Attack. Walk past the Beamos Statues to the end of the platform. Walk over to the right facing the bridge and position yourself so that the left half of Link is lined up with the small opening. Take out the Gale Boomerang, try to target between the gap, above the door frame, and Long Jump Attack. The speed of the attack will allow you to clip through the tiny gap as long as your sword doesn't bounce off the wall.

Skip the 2nd Key Shard

In the room before the second key shard, you can Long Jump Attack over to the door leading to the Dangoro fight. Simply run past the first spinning platform, turn right, R-Target over the top of the door frame with the Gale Boomerang and Long Jump Attack.

Magnet Skip

Setup by Hakua & gymnast86

Alternatively to using the magnet outside you can LJA across without having to activate the Magnet. Instead of using the initial LJA you can also do two jump attacks to get onto the railing, using the wooden block on the left.

The following is a variation on the above method.

You can also use this out of bounds movement to get over to the bridge area. This is around 10 seconds slower than the above method.

Room Before Fyrus

When you enter the room, it's easier to shoot the bridge down first so that you can run past the enemies, instead of walking down the path and being forced to kill the archers.